Did you check the fusible link as well? Then, measure the voltage across the battery with the motor off and then with it running (1500-2000 RPMs). With the motor running, the voltage should be .5-2.5 volts above the baseline. If not, you may have a defective alternator or you may have fried the PCM circuit(s).
The way it works, the L Control circuit on the PCM tells the regulator to turn on. The regulator then has to see the reference voltage through the Generator fuse to control the generator. When there's a problem, the regulator grounds the F Input circuit to the PCM which then turns on the battery warning light. There's a lot going on here and thus, if everything checks out as far as you can tell, you may want to consider taking it to a shop.